You do not need to use substring at all since your format
doesn't hold that info.
SimpleDateFormat format = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss");
String fechaStr = "2013-10-10 10:49:29.10000";
Date fechaNueva = format.parse(fechaStr);
System.out.println(format.format(fechaNueva)); // Prints 2013-10-10 10:49:29